// create from a dataset
public VariableBean(Variable vs) {
this.vs = vs;
// vs = (v instanceof VariableEnhanced) ? (VariableEnhanced) v : new VariableStandardized( v);
setName(vs.getShortName());
setDescription(vs.getDescription());
setUnits(vs.getUnitsString());
setDataType(vs.getDataType().toString());
// Attribute csAtt = vs.findAttribute("_coordSystems");
// if (csAtt != null)
// setCoordSys( csAtt.getStringValue());
// collect dimensions
StringBuilder lens = new StringBuilder();
StringBuilder names = new StringBuilder();
java.util.List dims = vs.getDimensions();
for (int j = 0; j < dims.size(); j++) {
ucar.nc2.Dimension dim = (ucar.nc2.Dimension) dims.get(j);
if (j > 0) {
lens.append(",");
names.append(",");
}
String name = dim.isShared() ? dim.getName() : "anon";
names.append(name);
lens.append(dim.getLength());
}
setDimensions(names.toString());
setShape(lens.toString());
}
/* Structure {
int LAT[0];
...
int LAT[149];
} IMAGE_LAT_ARRAY(3600);
type = Layout(8); type= 2 (chunked) storageSize = (1,600) dataSize=0 dataAddress=2548046
*/
@Test
public void testReadOneAtATime() throws java.io.IOException, InvalidRangeException {
try (NetcdfFile ncfile = TestH5.openH5("IASI/IASI.h5")) {
Variable dset = ncfile.findVariable("U-MARF/EPS/IASI_xxx_1C/DATA/IMAGE_LAT_ARRAY");
assert (null != dset);
assert (dset.getDataType() == DataType.STRUCTURE);
assert (dset.getRank() == 1);
assert (dset.getSize() == 3600);
Dimension d = dset.getDimension(0);
assert (d.getLength() == 3600);
Structure s = (Structure) dset;
// read last one - chunked
StructureData sd = s.readStructure(3599);
assert sd.getScalarInt("LAT[0]") == 70862722;
assert sd.getScalarInt("LAT[149]") == 85302263;
// read one at a time
for (int i = 3590; i < d.getLength(); i++) {
s.readStructure(i);
System.out.println(" read structure " + i);
}
}
System.out.println("*** testReadIASI ok");
}
// convert to shared dimensions
private void setSharedDimensions(
Variable v, List<Element> values, List<Dimension> unknownDims, String location) {
if (values.size() == 0) return;
// remove the "scalar" dumbension
Iterator<Element> iter = values.iterator();
while (iter.hasNext()) {
Element value = iter.next();
String dimName = value.getText().trim();
if (dimName.equalsIgnoreCase("scalar")) iter.remove();
}
// gotta have same number of dimensions
List<Dimension> oldDims = v.getDimensions();
if (oldDims.size() != values.size()) {
log.error("Different number of dimensions for {} {}", v, location);
return;
}
List<Dimension> newDims = new ArrayList<>();
Group group = v.getParentGroup();
for (int i = 0; i < values.size(); i++) {
Element value = values.get(i);
String dimName = value.getText().trim();
dimName = NetcdfFile.makeValidCdmObjectName(dimName);
Dimension dim = group.findDimension(dimName);
Dimension oldDim = oldDims.get(i);
if (dim == null) dim = checkUnknownDims(dimName, unknownDims, oldDim, location);
if (dim == null) {
log.error(
"Unknown Dimension= {} for variable = {} {} ", dimName, v.getFullName(), location);
return;
}
if (dim.getLength() != oldDim.getLength()) {
log.error(
"Shared dimension ("
+ dim.getShortName()
+ ") has different length than data dimension ("
+ oldDim.getShortName()
+ ") shared="
+ dim.getLength()
+ " org="
+ oldDim.getLength()
+ " for "
+ v
+ " "
+ location);
return;
}
newDims.add(dim);
}
v.setDimensions(newDims);
if (showWork) System.out.printf(" set shared dimensions for %s %n", v.getNameAndDimensions());
}
private boolean compare(List<Dimension> dims1, List<Dimension> dims2) {
if (dims1.size() != dims2.size()) return false;
for (int i = 0; i < dims1.size(); i++) {
Dimension dim1 = dims1.get(i);
Dimension dim2 = dims2.get(i);
// if (!dim1.getName().equals(dim2.getName())) return false;
if (dim1.getLength() != dim2.getLength()) return false;
}
return true;
}
/*
Structure {
int a_name;
byte b_name(3);
byte c_name(3);
short d_name(3);
int e_name(3);
long f_name(3);
int g_name(3);
short h_name(3);
int i_name(3);
long j_name(3);
float k_name(3);
double l_name(3);
} CompoundNative(15);
type = Layout(8); type= 1 (contiguous) storageSize = (15,144) dataSize=0 dataAddress=2048
*/
@Test
public void testReadH5StructureArrayMembers() throws java.io.IOException {
try (NetcdfFile ncfile = TestH5.openH5("complex/compound_native.h5")) {
Variable dset = ncfile.findVariable("CompoundNative");
assert (null != dset);
assert (dset.getDataType() == DataType.STRUCTURE);
assert (dset.getRank() == 1);
assert (dset.getSize() == 15);
Dimension d = dset.getDimension(0);
assert (d.getLength() == 15);
Structure s = (Structure) dset;
// read all with the iterator
StructureDataIterator iter = s.getStructureIterator();
while (iter.hasNext()) {
StructureData sd = iter.next();
for (StructureMembers.Member m : sd.getMembers()) {
Array data = sd.getArray(m);
NCdumpW.printArray(data, m.getName(), out, null);
}
}
}
System.out.println("*** testReadH5StructureArrayMembers ok");
}
// look if the wanted dimension is in the unknownDims list.
private Dimension checkUnknownDims(
String wantDim, List<Dimension> unknownDims, Dimension oldDim, String location) {
for (Dimension dim : unknownDims) {
if (dim.getShortName().equals(wantDim)) {
int len = oldDim.getLength();
if (len == 0) dim.setUnlimited(true); // allow zero length dimension !!
dim.setLength(len); // use existing (anon) dimension
Group parent = dim.getGroup();
parent.addDimensionIfNotExists(dim); // add to the parent
unknownDims.remove(dim); // remove from list LOOK is this ok?
log.warn("unknownDim {} length set to {}{}", wantDim, oldDim.getLength(), location);
return dim;
}
}
return null;
}
/** get the shape */
public int[] getShape() {
int[] shape = new int[mydims.size()];
for (int i = 0; i < mydims.size(); i++) {
Dimension d = mydims.get(i);
shape[i] = d.getLength();
}
return shape;
}
/** Create a DAS for this netcdf file */
NcDAS(NetcdfFile ncfile) {
// Variable attributes
Iterator iter = ncfile.getVariables().iterator();
while (iter.hasNext()) {
Variable v = (Variable) iter.next();
doVariable(v, null);
}
// Global attributes
opendap.dap.AttributeTable gtable = new opendap.dap.AttributeTable("NC_GLOBAL");
int count = addAttributes(gtable, null, ncfile.getGlobalAttributes().iterator());
if (count > 0)
try {
addAttributeTable("NC_GLOBAL", gtable);
} catch (AttributeExistsException e) {
log.error("Cant add NC_GLOBAL", e);
}
// unlimited dimension
iter = ncfile.getDimensions().iterator();
while (iter.hasNext()) {
Dimension d = (Dimension) iter.next();
if (d.isUnlimited()) {
opendap.dap.AttributeTable table = new opendap.dap.AttributeTable("DODS_EXTRA");
try {
table.appendAttribute("Unlimited_Dimension", opendap.dap.Attribute.STRING, d.getName());
addAttributeTable("DODS_EXTRA", table);
} catch (Exception e) {
log.error("Error adding Unlimited_Dimension =" + e);
}
break;
}
}
// unused dimensions
opendap.dap.AttributeTable dimTable = null;
iter = ncfile.getDimensions().iterator();
while (iter.hasNext()) {
Dimension d = (Dimension) iter.next();
if (null == usedDims.get(d.getName())) {
if (dimTable == null) dimTable = new opendap.dap.AttributeTable("EXTRA_DIMENSION");
try {
dimTable.appendAttribute(
d.getName(), opendap.dap.Attribute.INT32, Integer.toString(d.getLength()));
} catch (Exception e) {
log.error("Error adding Unlimited_Dimension =" + e);
}
}
}
if (dimTable != null)
try {
addAttributeTable("EXTRA_DIMENSION", dimTable);
} catch (AttributeExistsException e) {
log.error("Cant add EXTRA_DIMENSION", e);
}
}
public void testDimensions(NetcdfFile ncfile) {
System.out.println("ncfile = \n" + ncfile);
Dimension latDim = ncfile.findDimension("lat");
assert null != latDim;
assert latDim.getShortName().equals("lat");
assert latDim.getLength() == 3;
assert !latDim.isUnlimited();
Dimension lonDim = ncfile.findDimension("lon");
assert null != lonDim;
assert lonDim.getShortName().equals("lon");
assert lonDim.getLength() == 4;
assert !lonDim.isUnlimited();
Dimension timeDim = ncfile.findDimension("time");
assert null != timeDim;
assert timeDim.getShortName().equals("time");
assert timeDim.getLength() == 3 : timeDim.getLength();
}
/** Instances which have same contents are equal. Careful!! this is not object identity !! */
@Override
public boolean equals(Object oo) {
if (this == oo) return true;
if (!(oo instanceof Dimension)) return false;
Dimension other = (Dimension) oo;
if ((g != null) && !g.equals(other.getGroup())) return false;
if ((getName() == null) && (other.getName() != null)) return false;
if ((getName() != null) && !getName().equals(other.getName())) return false;
return (getLength() == other.getLength())
&& (isUnlimited() == other.isUnlimited())
&& (isVariableLength() == other.isVariableLength())
&& (isShared() == other.isShared());
}
/**
* Create a new GeoGrid that is a logical subset of this GeoGrid.
*
* @param t_range subset the time dimension, or null if you want all of it
* @param z_range subset the vertical dimension, or null if you want all of it
* @param bbox a lat/lon bounding box, or null if you want all x,y
* @param z_stride use only if z_range is null, then take all z with this stride (1 means all)
* @param y_stride use this stride on the y coordinate (1 means all)
* @param x_stride use this stride on the x coordinate (1 means all)
* @return subsetted GeoGrid
* @throws InvalidRangeException if bbox does not intersect GeoGrid
*/
public GeoGrid subset(
Range t_range, Range z_range, LatLonRect bbox, int z_stride, int y_stride, int x_stride)
throws InvalidRangeException {
if ((z_range == null) && (z_stride > 1)) {
Dimension zdim = getZDimension();
if (zdim != null) z_range = new Range(0, zdim.getLength() - 1, z_stride);
}
Range y_range = null, x_range = null;
if (bbox != null) {
List yx_ranges = gcs.getRangesFromLatLonRect(bbox);
y_range = (Range) yx_ranges.get(0);
x_range = (Range) yx_ranges.get(1);
}
if (y_stride > 1) {
if (y_range == null) {
Dimension ydim = getYDimension();
y_range = new Range(0, ydim.getLength() - 1, y_stride);
} else {
y_range = new Range(y_range.first(), y_range.last(), y_stride);
}
}
if (x_stride > 1) {
if (x_range == null) {
Dimension xdim = getXDimension();
x_range = new Range(0, xdim.getLength() - 1, x_stride);
} else {
x_range = new Range(x_range.first(), x_range.last(), x_stride);
}
}
return subset(t_range, z_range, y_range, x_range);
}
@Test
public void testH5StructureDS() throws java.io.IOException {
int a_name = 0;
String[] b_name =
new String[] {
"A fight is a contract that takes two people to honor.",
"A combative stance means that you've accepted the contract.",
"In which case, you deserve what you get.",
" -- Professor Cheng Man-ch'ing"
};
String c_name = "Hello!";
// H5header.setDebugFlags(new ucar.nc2.util.DebugFlagsImpl("H5header/header"));
try (NetcdfDataset ncfile =
NetcdfDataset.openDataset(TestH5.testDir + "complex/compound_complex.h5")) {
Variable dset = ncfile.findVariable("CompoundComplex");
assert (null != dset);
assert (dset.getDataType() == DataType.STRUCTURE);
assert (dset.getRank() == 1);
assert (dset.getSize() == 6);
Dimension d = dset.getDimension(0);
assert (d.getLength() == 6);
Structure s = (Structure) dset;
// read all with the iterator
StructureDataIterator iter = s.getStructureIterator();
while (iter.hasNext()) {
StructureData sd = iter.next();
assert sd.getScalarInt("a_name") == a_name;
a_name++;
assert sd.getScalarString("c_name").equals(c_name);
String[] results = sd.getJavaArrayString(sd.findMember("b_name"));
assert results.length == b_name.length;
int count = 0;
for (String r : results) assert r.equals(b_name[count++]);
for (StructureMembers.Member m : sd.getMembers()) {
Array data = sd.getArray(m);
NCdumpW.printArray(data, m.getName(), out, null);
}
}
}
System.out.println("*** testH5StructureDS ok");
}
private void createDataVariables(List<VariableSimpleIF> dataVars) throws IOException {
/* height variable
Variable heightVar = ncfile.addStringVariable(altName, recordDims, 20);
ncfile.addVariableAttribute(heightVar, new Attribute("long_name", "height of observation"));
ncfile.addVariableAttribute(heightVar, new Attribute("units", altUnits)); */
Variable v = ncfile.addVariable(parentProfileIndex, DataType.INT, recordDimName);
ncfile.addVariableAttribute(v, new Attribute("long_name", "index of parent profile"));
v = ncfile.addVariable(nextObsName, DataType.INT, recordDimName);
ncfile.addVariableAttribute(
v, new Attribute("long_name", "record number of next obs in linked list for this profile"));
// find all dimensions needed by the data variables
for (VariableSimpleIF var : dataVars) {
List<Dimension> dims = var.getDimensions();
dimSet.addAll(dims);
}
// add them
for (Dimension d : dimSet) {
if (!d.isUnlimited())
ncfile.addDimension(d.getName(), d.getLength(), d.isShared(), false, d.isVariableLength());
}
// add the data variables all using the record dimension
for (VariableSimpleIF oldVar : dataVars) {
List<Dimension> dims = oldVar.getDimensions();
StringBuffer dimNames = new StringBuffer(recordDimName);
for (Dimension d : dims) {
if (!d.isUnlimited()) dimNames.append(" ").append(d.getName());
}
Variable newVar =
ncfile.addVariable(oldVar.getName(), oldVar.getDataType(), dimNames.toString());
List<Attribute> atts = oldVar.getAttributes();
for (Attribute att : atts) {
ncfile.addVariableAttribute(newVar, att);
}
}
}
public VariableBean(VariableEnhanced v) {
this.ve = v;
setName(v.getFullName());
setDescription(v.getDescription());
setUnits(v.getUnitsString());
// collect dimensions
StringBuilder lens = new StringBuilder();
StringBuilder names = new StringBuilder();
java.util.List dims = v.getDimensions();
for (int j = 0; j < dims.size(); j++) {
ucar.nc2.Dimension dim = (ucar.nc2.Dimension) dims.get(j);
if (j > 0) {
lens.append(",");
names.append(",");
}
String name = dim.isShared() ? dim.getShortName() : "anon";
names.append(name);
lens.append(dim.getLength());
}
setDims(names.toString());
setShape(lens.toString());
StringBuilder buff = new StringBuilder();
List<CoordinateSystem> csList = v.getCoordinateSystems();
for (CoordinateSystem cs : csList) {
if (firstCoordSys == null) firstCoordSys = cs;
else buff.append("; ");
buff.append(cs.getName());
Formatter gridBuff = new Formatter();
if (GridCoordSys.isGridCoordSys(gridBuff, cs, v)) {
addDataType("grid");
} /* else if (PointDatasetDefaultHandler.isPointFeatureDataset(ds)) {
addDataType("point");
} */
}
setCoordSys(buff.toString());
}
public AxisBean(CoordinateAxis v) {
this.axis = v;
setName(v.getFullName());
setCoordVar(v.isCoordinateVariable());
setDescription(v.getDescription());
setUnits(v.getUnitsString());
// collect dimensions
StringBuilder lens = new StringBuilder();
StringBuilder names = new StringBuilder();
java.util.List dims = v.getDimensions();
for (int j = 0; j < dims.size(); j++) {
ucar.nc2.Dimension dim = (ucar.nc2.Dimension) dims.get(j);
if (j > 0) {
lens.append(",");
names.append(",");
}
String name = dim.isShared() ? dim.getShortName() : "anon";
names.append(name);
lens.append(dim.getLength());
}
setDims(names.toString());
setShape(lens.toString());
AxisType at = v.getAxisType();
if (at != null) setAxisType(at.toString());
String p = v.getPositive();
if (p != null) setPositive(p);
if (v instanceof CoordinateAxis1D) {
CoordinateAxis1D v1 = (CoordinateAxis1D) v;
if (v1.isRegular()) setRegular(Double.toString(v1.getIncrement()));
}
isLayer = (null != axis.findAttribute(_Coordinate.ZisLayer));
isInterval = axis.isInterval();
}
/* Structure {
char EntryName(64);
char Definition(1024);
char Unit(1024);
char Scale Factor(1024);
} TIME_DESCR(60);
type = Layout(8); type= 2 (chunked) storageSize = (1,3136) dataSize=0 dataAddress=684294
*/
@Test
public void testReadManyAtATime() throws java.io.IOException, InvalidRangeException {
try (NetcdfFile ncfile = TestH5.openH5("IASI/IASI.h5")) {
Variable dset = ncfile.findVariable("U-MARF/EPS/IASI_xxx_1C/DATA/TIME_DESCR");
assert (null != dset);
assert (dset.getDataType() == DataType.STRUCTURE);
assert (dset.getRank() == 1);
assert (dset.getSize() == 60);
Dimension d = dset.getDimension(0);
assert (d.getLength() == 60);
ArrayStructure data = (ArrayStructure) dset.read();
StructureMembers.Member m = data.getStructureMembers().findMember("EntryName");
assert m != null;
for (int i = 0; i < dset.getSize(); i++) {
String r = data.getScalarString(i, m);
if (i % 2 == 0) assert r.equals("TIME[" + i / 2 + "]-days") : r + " at " + i;
else assert r.equals("TIME[" + i / 2 + "]-milliseconds") : r + " at " + i;
}
}
System.out.println("*** testReadManyAtATime ok");
}
public int getRecordCount() {
Dimension unlimitedDim = ncfile.getUnlimitedDimension();
return unlimitedDim.getLength();
}
@Test
public void testDoradeAir() throws IOException {
System.out.println("**** Open " + airDoradeFile);
try (NetcdfFile ncfile = NetcdfFile.open(airDoradeFile)) {
for (Variable v : ncfile.getVariables()) {
System.out.println(v.getFullName());
}
Dimension gateDim = ncfile.getRootGroup().findDimension("gate_1");
assert (gateDim.getLength() == 320);
Dimension radialDim = ncfile.getRootGroup().findDimension("radial");
assert (radialDim.getLength() == 274);
Variable var;
var = ncfile.findVariable("elevation");
testReadData(var);
var = ncfile.findVariable("azimuth");
testReadData(var);
var = ncfile.findVariable("distance_1");
testReadData(var);
var = ncfile.findVariable("latitudes_1");
testReadData(var);
var = ncfile.findVariable("longitudes_1");
testReadData(var);
var = ncfile.findVariable("altitudes_1");
testReadData(var);
var = ncfile.findVariable("rays_time");
testReadData(var);
var = ncfile.findVariable("Range_to_First_Cell");
float t = testReadScalar(var);
assert (t == (float) -2.0);
var = ncfile.findVariable("Cell_Spacing");
t = testReadScalar(var);
assert (t == (float) 150.0);
var = ncfile.findVariable("Fixed_Angle");
t = testReadScalar(var);
assert (t == (float) -16.53);
var = ncfile.findVariable("Nyquist_Velocity");
t = testReadScalar(var);
assert (t == (float) 78.03032);
var = ncfile.findVariable("Unambiguous_Range");
t = testReadScalar(var);
assert (t == (float) 60.0);
var = ncfile.findVariable("Radar_Constant");
t = testReadScalar(var);
assert (t == (float) -81.17389);
var = ncfile.findVariable("rcvr_gain");
t = testReadScalar(var);
assert (t == (float) 32.64);
var = ncfile.findVariable("ant_gain");
t = testReadScalar(var);
assert (t == (float) 39.35);
var = ncfile.findVariable("sys_gain");
t = testReadScalar(var);
assert (t == (float) 52.34);
var = ncfile.findVariable("bm_width");
t = testReadScalar(var);
assert (t == (float) 1.79);
var = ncfile.findVariable("VS");
testReadData(var);
var = ncfile.findVariable("VL");
testReadData(var);
var = ncfile.findVariable("SW");
testReadData(var);
var = ncfile.findVariable("VR");
testReadData(var);
var = ncfile.findVariable("NCP");
testReadData(var);
var = ncfile.findVariable("DBZ");
testReadData(var);
var = ncfile.findVariable("VG");
testReadData(var);
var = ncfile.findVariable("VT");
testReadData(var);
assert (null != var.getDimension(0));
assert (null != var.getDimension(1));
}
}
private FeatureType amendGrid(
Element gridElem, NetcdfFile ncfile, Group parent, String location) {
List<Dimension> unknownDims = new ArrayList<>();
// always has x and y dimension
String xdimSizeS = gridElem.getChild("XDim").getText().trim();
String ydimSizeS = gridElem.getChild("YDim").getText().trim();
int xdimSize = Integer.parseInt(xdimSizeS);
int ydimSize = Integer.parseInt(ydimSizeS);
parent.addDimensionIfNotExists(new Dimension("XDim", xdimSize));
parent.addDimensionIfNotExists(new Dimension("YDim", ydimSize));
/* see HdfEosModisConvention
UpperLeftPointMtrs=(-20015109.354000,1111950.519667)
LowerRightMtrs=(-18903158.834333,-0.000000)
Projection=GCTP_SNSOID
ProjParams=(6371007.181000,0,0,0,0,0,0,0,0,0,0,0,0)
SphereCode=-1
*/
Element proj = gridElem.getChild("Projection");
if (proj != null) {
Variable crs = new Variable(ncfile, parent, null, HDFEOS_CRS);
crs.setDataType(DataType.SHORT);
crs.setDimensions(""); // scalar
crs.setCachedData(Array.makeArray(DataType.SHORT, 1, 0, 0)); // fake data
parent.addVariable(crs);
addAttributeIfExists(gridElem, HDFEOS_CRS_Projection, crs, false);
addAttributeIfExists(gridElem, HDFEOS_CRS_UpperLeft, crs, true);
addAttributeIfExists(gridElem, HDFEOS_CRS_LowerRight, crs, true);
addAttributeIfExists(gridElem, HDFEOS_CRS_ProjParams, crs, true);
addAttributeIfExists(gridElem, HDFEOS_CRS_SphereCode, crs, false);
}
// global Dimensions
Element d = gridElem.getChild("Dimension");
List<Element> dims = d.getChildren();
for (Element elem : dims) {
String name = elem.getChild("DimensionName").getText().trim();
name = NetcdfFile.makeValidCdmObjectName(name);
if (name.equalsIgnoreCase("scalar")) continue;
String sizeS = elem.getChild("Size").getText().trim();
int length = Integer.parseInt(sizeS);
Dimension old = parent.findDimension(name);
if ((old == null) || (old.getLength() != length)) {
if (length > 0) {
Dimension dim = new Dimension(name, length);
if (parent.addDimensionIfNotExists(dim) && showWork)
System.out.printf(" Add dimension %s %n", dim);
} else {
log.warn("Dimension {} has size {} {} ", sizeS, name, location);
Dimension udim = new Dimension(name, 1);
udim.setGroup(parent);
unknownDims.add(udim);
if (showWork) System.out.printf(" Add dimension %s %n", udim);
}
}
}
// Geolocation Variables
Group geoFieldsG = parent.findGroup(GEOLOC_FIELDS);
if (geoFieldsG == null) geoFieldsG = parent.findGroup(GEOLOC_FIELDS2);
if (geoFieldsG != null) {
Element floc = gridElem.getChild("GeoField");
List<Element> varsLoc = floc.getChildren();
for (Element elem : varsLoc) {
String varname = elem.getChild("GeoFieldName").getText().trim();
Variable v = geoFieldsG.findVariable(varname);
// if (v == null)
// v = geoFieldsG.findVariable( H4header.createValidObjectName(varname));
assert v != null : varname;
Element dimList = elem.getChild("DimList");
List<Element> values = dimList.getChildren("value");
setSharedDimensions(v, values, unknownDims, location);
}
}
// Data Variables
Group dataG = parent.findGroup(DATA_FIELDS);
if (dataG == null)
dataG =
parent.findGroup(
DATA_FIELDS2); // eg C:\data\formats\hdf4\eos\mopitt\MOP03M-200501-L3V81.0.1.hdf
if (dataG != null) {
Element f = gridElem.getChild("DataField");
List<Element> vars = f.getChildren();
for (Element elem : vars) {
String varname = elem.getChild("DataFieldName").getText().trim();
varname = NetcdfFile.makeValidCdmObjectName(varname);
Variable v = dataG.findVariable(varname);
// if (v == null)
// v = dataG.findVariable( H4header.createValidObjectName(varname));
assert v != null : varname;
Element dimList = elem.getChild("DimList");
List<Element> values = dimList.getChildren("value");
setSharedDimensions(v, values, unknownDims, location);
}
// get projection
String projS = null;
Element projElem = gridElem.getChild("Projection");
if (projElem != null) projS = projElem.getText().trim();
boolean isLatLon = "GCTP_GEO".equals(projS);
// look for XDim, YDim coordinate variables
if (isLatLon) {
for (Variable v : dataG.getVariables()) {
if (v.isCoordinateVariable()) {
if (v.getShortName().equals("YDim")) {
v.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lat.toString()));
v.addAttribute(new Attribute(CDM.UNITS, CDM.LAT_UNITS));
}
if (v.getShortName().equals("XDim"))
v.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lon.toString()));
}
}
}
}
return FeatureType.GRID;
}
private FeatureType amendSwath(NetcdfFile ncfile, Element swathElem, Group parent) {
FeatureType featureType = FeatureType.SWATH;
List<Dimension> unknownDims = new ArrayList<>();
// Dimensions
Element d = swathElem.getChild("Dimension");
List<Element> dims = d.getChildren();
for (Element elem : dims) {
String name = elem.getChild("DimensionName").getText().trim();
name = NetcdfFile.makeValidCdmObjectName(name);
if (name.equalsIgnoreCase("scalar")) continue;
String sizeS = elem.getChild("Size").getText().trim();
int length = Integer.parseInt(sizeS);
if (length > 0) {
Dimension dim = parent.findDimensionLocal(name);
if (dim != null) { // already added - may be dimension scale ?
if (dim.getLength() != length) { // ok as long as it matches
log.error("Conflicting Dimensions = {} {}", dim, ncfile.getLocation());
throw new IllegalStateException("Conflicting Dimensions = " + name);
}
} else {
dim = new Dimension(name, length);
if (parent.addDimensionIfNotExists(dim) && showWork)
System.out.printf(" Add dimension %s %n", dim);
}
} else {
log.warn("Dimension " + name + " has size " + sizeS, ncfile.getLocation());
Dimension udim = new Dimension(name, 1);
udim.setGroup(parent);
unknownDims.add(udim);
if (showWork) System.out.printf(" Add dimension %s %n", udim);
}
}
// Dimension Maps
Element dmap = swathElem.getChild("DimensionMap");
List<Element> dimMaps = dmap.getChildren();
for (Element elem : dimMaps) {
String geoDimName = elem.getChild("GeoDimension").getText().trim();
geoDimName = NetcdfFile.makeValidCdmObjectName(geoDimName);
String dataDimName = elem.getChild("DataDimension").getText().trim();
dataDimName = NetcdfFile.makeValidCdmObjectName(dataDimName);
String offsetS = elem.getChild("Offset").getText().trim();
String incrS = elem.getChild("Increment").getText().trim();
int offset = Integer.parseInt(offsetS);
int incr = Integer.parseInt(incrS);
// make new variable for this dimension map
Variable v = new Variable(ncfile, parent, null, dataDimName);
v.setDimensions(geoDimName);
v.setDataType(DataType.INT);
int npts = (int) v.getSize();
Array data = Array.makeArray(v.getDataType(), npts, offset, incr);
v.setCachedData(data, true);
v.addAttribute(new Attribute("_DimensionMap", ""));
parent.addVariable(v);
if (showWork) System.out.printf(" Add dimensionMap %s %n", v);
}
// Geolocation Variables
Group geoFieldsG = parent.findGroup(GEOLOC_FIELDS);
if (geoFieldsG == null) geoFieldsG = parent.findGroup(GEOLOC_FIELDS2);
if (geoFieldsG != null) {
Variable latAxis = null, lonAxis = null;
Element floc = swathElem.getChild("GeoField");
List<Element> varsLoc = floc.getChildren();
for (Element elem : varsLoc) {
String varname = elem.getChild("GeoFieldName").getText().trim();
Variable v = geoFieldsG.findVariable(varname);
// if (v == null)
// v = geoFieldsG.findVariable( H4header.createValidObjectName(varname));
assert v != null : varname;
AxisType axis = addAxisType(ncfile, v);
if (axis == AxisType.Lat) latAxis = v;
if (axis == AxisType.Lon) lonAxis = v;
Element dimList = elem.getChild("DimList");
List<Element> values = dimList.getChildren("value");
setSharedDimensions(v, values, unknownDims, ncfile.getLocation());
if (showWork) System.out.printf(" set coordinate %s %n", v);
}
if ((latAxis != null) && (lonAxis != null)) {
List<Dimension> xyDomain = CoordinateSystem.makeDomain(new Variable[] {latAxis, lonAxis});
if (xyDomain.size() < 2) featureType = FeatureType.PROFILE; // ??
}
}
// Data Variables
Group dataG = parent.findGroup(DATA_FIELDS);
if (dataG == null) dataG = parent.findGroup(DATA_FIELDS2);
if (dataG != null) {
Element f = swathElem.getChild("DataField");
List<Element> vars = f.getChildren();
for (Element elem : vars) {
Element dataFieldNameElem = elem.getChild("DataFieldName");
if (dataFieldNameElem == null) continue;
String varname = NetcdfFile.makeValidCdmObjectName(dataFieldNameElem.getText().trim());
Variable v = dataG.findVariable(varname);
// if (v == null)
// v = dataG.findVariable( H4header.createValidObjectName(varname));
if (v == null) {
log.error("Cant find variable {} {}", varname, ncfile.getLocation());
continue;
}
Element dimList = elem.getChild("DimList");
List<Element> values = dimList.getChildren("value");
setSharedDimensions(v, values, unknownDims, ncfile.getLocation());
}
}
return featureType;
}
public void testWritePermute() throws Exception {
NetcdfFileWriteable ncfile = new NetcdfFileWriteable();
ncfile.setName(TestLocal.cdmTestDataDir + "permuteTest.nc");
// define dimensions
Dimension xDim = ncfile.addDimension("x", 3);
Dimension yDim = ncfile.addDimension("y", 5);
Dimension zDim = ncfile.addDimension("z", 4);
Dimension tDim = ncfile.addDimension("time", 2);
// define Variables
ncfile.addVariable("time", double.class, new Dimension[] {tDim});
ncfile.addVariableAttribute("time", "units", "secs since 1-1-1 00:00");
ncfile.addVariable("z", double.class, new Dimension[] {zDim});
ncfile.addVariableAttribute("z", "units", "meters");
ncfile.addVariableAttribute("z", "positive", "up");
ncfile.addVariable("y", double.class, new Dimension[] {yDim});
ncfile.addVariableAttribute("y", "units", "degrees_north");
ncfile.addVariable("x", double.class, new Dimension[] {xDim});
ncfile.addVariableAttribute("x", "units", "degrees_east");
ncfile.addVariable("tzyx", double.class, new Dimension[] {tDim, zDim, yDim, xDim});
ncfile.addVariableAttribute("tzyx", "units", "K");
ncfile.addVariable("tzxy", double.class, new Dimension[] {tDim, zDim, xDim, yDim});
ncfile.addVariableAttribute("tzxy", "units", "K");
ncfile.addVariable("tyxz", double.class, new Dimension[] {tDim, yDim, xDim, zDim});
ncfile.addVariableAttribute("tyxz", "units", "K");
ncfile.addVariable("txyz", double.class, new Dimension[] {tDim, xDim, yDim, zDim});
ncfile.addVariableAttribute("txyz", "units", "K");
ncfile.addVariable("zyxt", double.class, new Dimension[] {zDim, yDim, xDim, tDim});
ncfile.addVariableAttribute("zyxt", "units", "K");
ncfile.addVariable("zxyt", double.class, new Dimension[] {zDim, xDim, yDim, tDim});
ncfile.addVariableAttribute("zxyt", "units", "K");
ncfile.addVariable("yxzt", double.class, new Dimension[] {yDim, xDim, zDim, tDim});
ncfile.addVariableAttribute("yxzt", "units", "K");
ncfile.addVariable("xyzt", double.class, new Dimension[] {xDim, yDim, zDim, tDim});
ncfile.addVariableAttribute("xyzt", "units", "K");
// missing one dimension
ncfile.addVariable("zyx", double.class, new Dimension[] {zDim, yDim, xDim});
ncfile.addVariable("txy", double.class, new Dimension[] {tDim, xDim, yDim});
ncfile.addVariable("yxz", double.class, new Dimension[] {yDim, xDim, zDim});
ncfile.addVariable("xzy", double.class, new Dimension[] {xDim, zDim, yDim});
ncfile.addVariable("yxt", double.class, new Dimension[] {yDim, xDim, tDim});
ncfile.addVariable("xyt", double.class, new Dimension[] {xDim, yDim, tDim});
ncfile.addVariable("xyz", double.class, new Dimension[] {xDim, yDim, zDim});
// missing two dimension
ncfile.addVariable("yx", double.class, new Dimension[] {yDim, xDim});
ncfile.addVariable("xy", double.class, new Dimension[] {xDim, yDim});
ncfile.addVariable("yz", double.class, new Dimension[] {yDim, zDim});
ncfile.addVariable("xz", double.class, new Dimension[] {xDim, zDim});
ncfile.addVariable("yt", double.class, new Dimension[] {yDim, tDim});
ncfile.addVariable("xt", double.class, new Dimension[] {xDim, tDim});
ncfile.addVariable("ty", double.class, new Dimension[] {tDim, yDim});
ncfile.addVariable("tx", double.class, new Dimension[] {tDim, xDim});
// add global attributes
ncfile.addGlobalAttribute("Convention", "COARDS");
// create the file
try {
ncfile.create();
} catch (IOException e) {
System.err.println("ERROR creating file");
assert (false);
}
// write time data
int len = tDim.getLength();
ArrayDouble A = new ArrayDouble.D1(len);
Index ima = A.getIndex();
for (int i = 0; i < len; i++) A.setDouble(ima.set(i), (double) (i * 3600));
int[] origin = new int[1];
try {
ncfile.write("time", origin, A);
} catch (IOException e) {
System.err.println("ERROR writing time");
assert (false);
}
// write z data
len = zDim.getLength();
A = new ArrayDouble.D1(len);
ima = A.getIndex();
for (int i = 0; i < len; i++) A.setDouble(ima.set(i), (double) (i * 10));
try {
ncfile.write("z", origin, A);
} catch (IOException e) {
System.err.println("ERROR writing z");
assert (false);
}
// write y data
len = yDim.getLength();
A = new ArrayDouble.D1(len);
ima = A.getIndex();
for (int i = 0; i < len; i++) A.setDouble(ima.set(i), (double) (i * 3));
try {
ncfile.write("y", origin, A);
} catch (IOException e) {
System.err.println("ERROR writing y");
assert (false);
}
// write x data
len = xDim.getLength();
A = new ArrayDouble.D1(len);
ima = A.getIndex();
for (int i = 0; i < len; i++) A.setDouble(ima.set(i), (double) (i * 5));
try {
ncfile.write("x", origin, A);
} catch (IOException e) {
System.err.println("ERROR writing x");
assert (false);
}
// write tzyx data
doWrite4(ncfile, "tzyx");
doWrite4(ncfile, "tzxy");
doWrite4(ncfile, "txyz");
doWrite4(ncfile, "tyxz");
doWrite4(ncfile, "zyxt");
doWrite4(ncfile, "zxyt");
doWrite4(ncfile, "xyzt");
doWrite4(ncfile, "yxzt");
doWrite3(ncfile, "zyx");
doWrite3(ncfile, "txy");
doWrite3(ncfile, "yxz");
doWrite3(ncfile, "xzy");
doWrite3(ncfile, "yxt");
doWrite3(ncfile, "xyt");
doWrite3(ncfile, "yxt");
doWrite3(ncfile, "xyz");
doWrite2(ncfile, "yx");
doWrite2(ncfile, "xy");
doWrite2(ncfile, "yz");
doWrite2(ncfile, "xz");
doWrite2(ncfile, "yt");
doWrite2(ncfile, "xt");
doWrite2(ncfile, "ty");
doWrite2(ncfile, "tx");
if (show) System.out.println("ncfile = " + ncfile);
// all done
try {
ncfile.close();
} catch (IOException e) {
System.err.println("ERROR writing file");
assert (false);
}
System.out.println("*****************Test Write done");
}
public void testWriteStandardVar() throws Exception {
NetcdfFileWriteable ncfile = new NetcdfFileWriteable(filename, false);
// define dimensions
Dimension latDim = ncfile.addDimension("lat", 2);
Dimension lonDim = ncfile.addDimension("lon", 3);
ArrayList dims = new ArrayList();
dims.add(latDim);
dims.add(lonDim);
// case 1
ncfile.addVariable("t1", DataType.DOUBLE, dims);
ncfile.addVariableAttribute("t1", CDM.SCALE_FACTOR, new Double(2.0));
ncfile.addVariableAttribute("t1", "add_offset", new Double(77.0));
// case 2
ncfile.addVariable("t2", DataType.BYTE, dims);
ncfile.addVariableAttribute("t2", CDM.SCALE_FACTOR, new Short((short) 2));
ncfile.addVariableAttribute("t2", "add_offset", new Short((short) 77));
// case 3
ncfile.addVariable("t3", DataType.BYTE, dims);
ncfile.addVariableAttribute("t3", "_FillValue", new Byte((byte) 255));
// case 4
ncfile.addVariable("t4", DataType.SHORT, dims);
ncfile.addVariableAttribute("t4", CDM.MISSING_VALUE, new Short((short) -9999));
// case 5
ncfile.addVariable("t5", DataType.SHORT, dims);
ncfile.addVariableAttribute("t5", CDM.MISSING_VALUE, new Short((short) -9999));
ncfile.addVariableAttribute("t5", CDM.SCALE_FACTOR, new Short((short) 2));
ncfile.addVariableAttribute("t5", "add_offset", new Short((short) 77));
// case 1
ncfile.addVariable("m1", DataType.DOUBLE, dims);
ncfile.addVariableAttribute("m1", CDM.MISSING_VALUE, -999.99);
// create the file
ncfile.create();
// write t1
ArrayDouble A = new ArrayDouble.D2(latDim.getLength(), lonDim.getLength());
int i, j;
Index ima = A.getIndex();
// write
for (i = 0; i < latDim.getLength(); i++)
for (j = 0; j < lonDim.getLength(); j++) A.setDouble(ima.set(i, j), (double) (i * 10.0 + j));
int[] origin = new int[2];
ncfile.write("t1", origin, A);
// write t2
ArrayByte Ab = new ArrayByte.D2(latDim.getLength(), lonDim.getLength());
ima = Ab.getIndex();
for (i = 0; i < latDim.getLength(); i++)
for (j = 0; j < lonDim.getLength(); j++) Ab.setByte(ima.set(i, j), (byte) (i * 10 + j));
ncfile.write("t2", origin, Ab);
// write t3
ncfile.write("t3", origin, Ab);
// write t4
Array As = new ArrayShort.D2(latDim.getLength(), lonDim.getLength());
ima = As.getIndex();
for (i = 0; i < latDim.getLength(); i++)
for (j = 0; j < lonDim.getLength(); j++) As.setShort(ima.set(i, j), (short) (i * 10 + j));
ncfile.write("t4", origin, As);
As.setShort(ima.set(0, 0), (short) -9999);
ncfile.write("t5", origin, As);
// write m1
ArrayDouble.D2 Ad = new ArrayDouble.D2(latDim.getLength(), lonDim.getLength());
for (i = 0; i < latDim.getLength(); i++)
for (j = 0; j < lonDim.getLength(); j++) Ad.setDouble(ima.set(i, j), (double) (i * 10.0 + j));
Ad.set(1, 1, -999.99);
ncfile.write("m1", new int[2], Ad);
// all done
ncfile.close();
System.out.println("**************TestStandardVar Write done");
}
@Override
public Product createProduct() throws ProductIOException {
int[] dims;
int sceneHeight = 0;
int sceneWidth = 0;
Group geodata = ncFile.findGroup("geophysical_data");
if (productReader.getProductType() == SeadasProductReader.ProductType.OISST) {
dims = ncFile.getVariables().get(4).getShape();
sceneHeight = dims[2];
sceneWidth = dims[3];
mustFlipY = true;
} else if (productReader.getProductType() == SeadasProductReader.ProductType.ANCCLIM) {
List<Variable> vars = ncFile.getVariables();
for (Variable v : vars) {
if (v.getRank() == 2) {
dims = v.getShape();
sceneHeight = dims[0];
sceneWidth = dims[1];
}
}
} else {
if (geodata != null) {
dims = geodata.getVariables().get(0).getShape();
sceneHeight = dims[0];
sceneWidth = dims[1];
} else {
ucar.nc2.Dimension latdim = ncFile.findDimension("lat");
ucar.nc2.Dimension londim = ncFile.findDimension("lon");
if (latdim != null) {
sceneHeight = latdim.getLength();
sceneWidth = londim.getLength();
} else {
dims = ncFile.getVariables().get(0).getShape();
sceneHeight = dims[0];
sceneWidth = dims[1];
}
}
}
String productName = productReader.getInputFile().getName();
try {
productName = getStringAttribute("Product_Name");
} catch (Exception ignored) {
}
SeadasProductReader.ProductType productType = productReader.getProductType();
Product product = new Product(productName, productType.toString(), sceneWidth, sceneHeight);
product.setDescription(productName);
product.setFileLocation(productReader.getInputFile());
product.setProductReader(productReader);
addGlobalMetadata(product);
addSmiMetadata(product);
// variableMap = addBands(product, ncFile.getVariables());
variableMap = addSmiBands(product, ncFile.getVariables());
try {
addGeocoding(product);
} catch (Exception ignored) {
}
addFlagsAndMasks(product);
if (productReader.getProductType() == SeadasProductReader.ProductType.Bathy) {
mustFlipY = true;
Dimension tileSize = new Dimension(640, 320);
product.setPreferredTileSize(tileSize);
}
return product;
}
@Test
public void testDoradeGround() throws IOException {
System.out.println("**** Open " + groundDoradeFile);
try (NetcdfFile ncfile = NetcdfFile.open(groundDoradeFile)) {
for (Variable v : ncfile.getVariables()) {
System.out.println(v.getFullName());
}
/* test both gate and radial dimension */
Dimension gateDim = ncfile.getRootGroup().findDimension("gate_1");
assert (gateDim.getLength() == 1008);
Dimension radialDim = ncfile.getRootGroup().findDimension("radial");
assert (radialDim.getLength() == 439);
/* test some att */
Attribute testAtt = ncfile.getRootGroup().findAttribute("Conventions");
assert (testAtt.getStringValue().equals(_Coordinate.Convention));
testAtt = ncfile.getRootGroup().findAttribute("format");
assert (testAtt.getStringValue().equals("Unidata/netCDF/Dorade"));
testAtt = ncfile.getRootGroup().findAttribute("Project_name");
assert (testAtt.getStringValue().equalsIgnoreCase("IHOP_2002"));
testAtt = ncfile.getRootGroup().findAttribute("Radar_Name");
assert (testAtt.getStringValue().equalsIgnoreCase("SPOL"));
testAtt = ncfile.getRootGroup().findAttribute("VolumeCoveragePatternName");
assert (testAtt.getStringValue().equalsIgnoreCase("SUR"));
testAtt = ncfile.getRootGroup().findAttribute("Volume_Number");
assert (testAtt.getStringValue().equalsIgnoreCase("1"));
testAtt = ncfile.getRootGroup().findAttribute("Sweep_Number");
assert (testAtt.getStringValue().equalsIgnoreCase("2"));
testAtt = ncfile.getRootGroup().findAttribute("Sweep_Date");
assert (testAtt.getStringValue().equalsIgnoreCase("2002-05-11 01:58:15Z"));
Variable var;
var = ncfile.findVariable("elevation");
testReadData(var);
var = ncfile.findVariable("azimuth");
testReadData(var);
var = ncfile.findVariable("distance_1");
testReadData(var);
var = ncfile.findVariable("latitudes_1");
testReadData(var);
var = ncfile.findVariable("longitudes_1");
testReadData(var);
var = ncfile.findVariable("altitudes_1");
testReadData(var);
var = ncfile.findVariable("rays_time");
testReadData(var);
var = ncfile.findVariable("Range_to_First_Cell");
float t = testReadScalar(var);
assert (t == (float) 150.0);
var = ncfile.findVariable("Cell_Spacing");
t = testReadScalar(var);
assert (t == (float) 149.89624);
var = ncfile.findVariable("Fixed_Angle");
t = testReadScalar(var);
assert (t == (float) 1.1975098);
var = ncfile.findVariable("Nyquist_Velocity");
t = testReadScalar(var);
assert (t == (float) 25.618269);
var = ncfile.findVariable("Unambiguous_Range");
t = testReadScalar(var);
assert (t == (float) 156.11694);
var = ncfile.findVariable("Radar_Constant");
t = testReadScalar(var);
assert (t == (float) 70.325195);
var = ncfile.findVariable("rcvr_gain");
t = testReadScalar(var);
assert (t == (float) 46.95);
var = ncfile.findVariable("ant_gain");
t = testReadScalar(var);
assert (t == (float) 45.58);
var = ncfile.findVariable("sys_gain");
t = testReadScalar(var);
assert (t == (float) 46.95);
var = ncfile.findVariable("bm_width");
t = testReadScalar(var);
assert (t == (float) 0.92);
var = ncfile.findVariable("VE");
testReadData(var);
var = ncfile.findVariable("DM");
testReadData(var);
var = ncfile.findVariable("NCP");
testReadData(var);
var = ncfile.findVariable("SW");
testReadData(var);
var = ncfile.findVariable("DZ");
testReadData(var);
var = ncfile.findVariable("DCZ");
testReadData(var);
var = ncfile.findVariable("LVDR");
testReadData(var);
var = ncfile.findVariable("NIQ");
testReadData(var);
var = ncfile.findVariable("AIQ");
testReadData(var);
var = ncfile.findVariable("CH");
testReadData(var);
var = ncfile.findVariable("AH");
testReadData(var);
var = ncfile.findVariable("CV");
testReadData(var);
var = ncfile.findVariable("AV");
testReadData(var);
var = ncfile.findVariable("RHOHV");
testReadData(var);
var = ncfile.findVariable("LDR");
testReadData(var);
var = ncfile.findVariable("DL");
testReadData(var);
var = ncfile.findVariable("DX");
testReadData(var);
var = ncfile.findVariable("ZDR");
testReadData(var);
var = ncfile.findVariable("PHI");
testReadData(var);
var = ncfile.findVariable("KDP");
testReadData(var);
assert (0 == var.findDimensionIndex("radial"));
assert (1 == var.findDimensionIndex("gate_1"));
}
}
/**
* Parses a variable recursively into appropriate ViewVariable implementations
*
* @throws IOException
* @throws
*/
private static AbstractViewVariable parseVariableRecursive(Variable var) throws IOException {
List<Dimension> dimensions = var.getDimensions();
// A single dimension means we can parse a SimpleAxis
if (dimensions.size() == 1) {
SimpleAxis axis =
new SimpleAxis(var.getName(), var.getDataType().name(), var.getUnitsString(), null, null);
Dimension d = dimensions.get(0);
axis.setDimensionBounds(new SimpleBounds(0, d.getLength()));
// Read our first and last values
Array first = null, last = null;
try {
first = var.read(new int[] {0}, new int[] {1});
last = var.read(new int[] {d.getLength() - 1}, new int[] {1});
} catch (InvalidRangeException ex) {
throw new IllegalArgumentException(
String.format("Unable to read variable ranges '%1$s'", var), ex);
}
axis.setValueBounds(new SimpleBounds(first.getDouble(0), last.getDouble(0)));
return axis;
// Otherwise we have a multi dimensional variable that we can parse as a grid
} else if (dimensions.size() > 0) {
SimpleGrid grid =
new SimpleGrid(var.getName(), var.getDataType().name(), var.getUnitsString(), null);
List<AbstractViewVariable> childAxes = new ArrayList<>();
// Recursively parse each dimension (which should map to a variable in the parent group)
for (Dimension d : dimensions) {
Variable mappedVariable = d.getGroup().findVariable(d.getName());
if (mappedVariable == null) {
// If the dimension doesn't map to a variable, we can't pull much information out of it
// So instead we'll have to introduce an axis that only includes dimension bounds
log.warn(
String.format(
"Dimension '%1$s' has no matching variable in parent group '%2$s'",
d, d.getGroup()));
SimpleAxis axis = new SimpleAxis(d.getName(), DataType.FLOAT.name(), "????", null, null);
axis.setDimensionBounds(new SimpleBounds(0, d.getLength() - 1));
childAxes.add(axis);
} else {
AbstractViewVariable parsedVar = parseVariableRecursive(mappedVariable);
if (parsedVar != null) childAxes.add(parsedVar);
}
}
if (childAxes.size() > 0) {
grid.setAxes(childAxes.toArray(new AbstractViewVariable[childAxes.size()]));
return grid;
} else {
return null;
}
} else {
// Currently unsupported...
log.warn(
String.format("Variables with 0 dimensions are currently unsupported. var='%1$s'", var));
return null;
}
}
public static void main2(String args[]) throws Exception {
final int NLVL = 2;
final int NLAT = 6;
final int NLON = 12;
final int NumberOfRecords = 2;
final float SAMPLE_PRESSURE = 900.0f;
final float SAMPLE_TEMP = 9.0f;
final float START_LAT = 25.0f;
final float START_LON = -125.0f;
// Create the file.
String filename = "pres_temp_4D.nc";
NetcdfFileWriteable dataFile = null;
try {
// Create new netcdf-3 file with the given filename
dataFile = NetcdfFileWriteable.createNew(filename, false);
// add dimensions where time dimension is unlimit
Dimension lvlDim = dataFile.addDimension("level", NLVL);
Dimension latDim = dataFile.addDimension("latitude", NLAT);
Dimension lonDim = dataFile.addDimension("longitude", NLON);
Dimension timeDim = dataFile.addDimension("time", 1000); // should
// not be
// need
// second
// argument
ArrayList dims = null;
// Define the coordinate variables.
dataFile.addVariable("latitude", DataType.FLOAT, new Dimension[] {latDim});
dataFile.addVariable("longitude", DataType.FLOAT, new Dimension[] {lonDim});
// Define units attributes for data variables.
dataFile.addVariableAttribute("latitude", "units", "degrees_north");
dataFile.addVariableAttribute("longitude", "units", "degrees_east");
// Define the netCDF variables for the pressure and temperature
// data.
dims = new ArrayList();
dims.add(timeDim);
dims.add(lvlDim);
dims.add(latDim);
dims.add(lonDim);
dataFile.addVariable("pressure", DataType.FLOAT, dims);
dataFile.addVariable("temperature", DataType.FLOAT, dims);
// Define units attributes for data variables.
dataFile.addVariableAttribute("pressure", "units", "hPa");
dataFile.addVariableAttribute("temperature", "units", "celsius");
// Create some pretend data. If this wasn't an example program, we
// would have some real data to write for example, model output.
ArrayFloat.D1 lats = new ArrayFloat.D1(latDim.getLength());
ArrayFloat.D1 lons = new ArrayFloat.D1(lonDim.getLength());
int i, j;
for (i = 0; i < latDim.getLength(); i++) {
lats.set(i, START_LAT + 5.f * i);
}
for (j = 0; j < lonDim.getLength(); j++) {
lons.set(j, START_LON + 5.f * j);
}
// Create the pretend data. This will write our surface pressure and
// surface temperature data.
ArrayFloat.D4 dataTemp =
new ArrayFloat.D4(
NumberOfRecords, lvlDim.getLength(), latDim.getLength(), lonDim.getLength());
ArrayFloat.D4 dataPres =
new ArrayFloat.D4(
NumberOfRecords, lvlDim.getLength(), latDim.getLength(), lonDim.getLength());
for (int record = 0; record < NumberOfRecords; record++) {
i = 0;
for (int lvl = 0; lvl < NLVL; lvl++)
for (int lat = 0; lat < NLAT; lat++)
for (int lon = 0; lon < NLON; lon++) {
dataPres.set(record, lvl, lat, lon, SAMPLE_PRESSURE + i);
dataTemp.set(record, lvl, lat, lon, SAMPLE_TEMP + i++);
}
}
// Create the file. At this point the (empty) file will be written
// to disk
dataFile.create();
// A newly created Java integer array to be initialized to zeros.
int[] origin = new int[4];
dataFile.write("latitude", lats);
dataFile.write("longitude", lons);
dataFile.write("pressure", origin, dataPres);
dataFile.write("temperature", origin, dataTemp);
dataFile.close();
} catch (IOException e) {
e.printStackTrace(System.err);
} catch (InvalidRangeException e) {
e.printStackTrace(System.err);
} finally {
// if (dataFile != null) {
// try {
// dataFile.close();
// } catch (IOException ioe) {
// ioe.printStackTrace();
// }
// }
}
System.out.println("*** SUCCESS writing example file " + filename);
}
public static void main(String args[]) throws Exception {
long start = System.currentTimeMillis();
Map<String, ucar.unidata.geoloc.Station> staHash =
new HashMap<String, ucar.unidata.geoloc.Station>();
String location = "R:/testdata/sounding/netcdf/Upperair_20070401_0000.nc";
NetcdfDataset ncfile = NetcdfDataset.openDataset(location);
ncfile.sendIospMessage(NetcdfFile.IOSP_MESSAGE_ADD_RECORD_STRUCTURE);
// look through record varibles, for those that have "manLevel" dimension
// make a StructureData object for those
StructureMembers sm = new StructureMembers("manLevel");
Dimension manDim = ncfile.findDimension("manLevel");
Structure record = (Structure) ncfile.findVariable("record");
List<Variable> allList = record.getVariables();
List<VariableSimpleIF> varList = new ArrayList<VariableSimpleIF>();
for (Variable v : allList) {
if ((v.getRank() == 1) && v.getDimension(0).equals(manDim)) {
// public VariableDS(NetcdfDataset ds, Group group, Structure parentStructure, String
// shortName, DataType dataType,
// String dims, String units, String desc) {
varList.add(
new VariableDS(
ncfile,
null,
null,
v.getShortName(),
v.getDataType(),
"",
v.getUnitsString(),
v.getDescription()));
// (String name, String desc, String units, DataType dtype, int []shape)
sm.addMember(
v.getShortName(),
v.getDescription(),
v.getUnitsString(),
v.getDataType(),
new int[0]); // scalar
}
}
ArrayStructureMA manAS = new ArrayStructureMA(sm, new int[] {manDim.getLength()});
// need the date units
Variable time = ncfile.findVariable("synTime");
String timeUnits = ncfile.findAttValueIgnoreCase(time, "units", null);
timeUnits = StringUtil.remove(timeUnits, '('); // crappy fsl'ism
timeUnits = StringUtil.remove(timeUnits, ')');
DateUnit timeUnit = new DateUnit(timeUnits);
// extract stations
int nrecs = 0;
StructureDataIterator iter = record.getStructureIterator();
while (iter.hasNext()) {
StructureData sdata = iter.next();
String name = sdata.getScalarString("staName");
ucar.unidata.geoloc.Station s = staHash.get(name);
if (s == null) {
float lat = sdata.convertScalarFloat("staLat");
float lon = sdata.convertScalarFloat("staLon");
float elev = sdata.convertScalarFloat("staElev");
s = new StationImpl(name, "", lat, lon, elev);
staHash.put(name, s);
}
nrecs++;
}
List<ucar.unidata.geoloc.Station> stnList =
Arrays.asList(staHash.values().toArray(new ucar.unidata.geoloc.Station[staHash.size()]));
Collections.sort(stnList);
// create the writer
WriterProfileObsDataset writer =
new WriterProfileObsDataset(location + ".out", "rewrite " + location);
writer.writeHeader(stnList, varList, nrecs, "prMan");
// extract records
iter = record.getStructureIterator();
while (iter.hasNext()) {
StructureData sdata = iter.next();
String name = sdata.getScalarString("staName");
double timeValue = sdata.convertScalarDouble("synTime");
Date date = timeUnit.makeDate(timeValue);
// transfer to the ArrayStructure
List<String> names = sm.getMemberNames();
for (String mname : names) {
manAS.setMemberArray(mname, sdata.getArray(mname));
}
// each level is weritten as a seperate structure
int numMand = sdata.getScalarInt("numMand");
if (numMand >= manDim.getLength()) continue;
for (int i = 0; i < numMand; i++) {
StructureData useData = manAS.getStructureData(i);
writer.writeRecord(name, date, useData);
}
}
writer.finish();
long took = System.currentTimeMillis() - start;
System.out.println("That took = " + took);
}
/**
* This reads an arbitrary data slice, returning the data in canonical order (rt-e-t-z-y-x). If
* any dimension does not exist, ignore it.
*
* @param rt if < 0, get all of runtime dim; if valid index, fix slice to that value.
* @param e if < 0, get all of ensemble dim; if valid index, fix slice to that value.
* @param t if < 0, get all of time dim; if valid index, fix slice to that value.
* @param z if < 0, get all of z dim; if valid index, fix slice to that value.
* @param y if < 0, get all of y dim; if valid index, fix slice to that value.
* @param x if < 0, get all of x dim; if valid index, fix slice to that value.
* @return data[rt,e,t,z,y,x], eliminating missing or fixed dimension.
*/
public Array readDataSlice(int rt, int e, int t, int z, int y, int x) throws java.io.IOException {
int rank = vs.getRank();
int[] start = new int[rank];
int[] shape = new int[rank];
for (int i = 0; i < rank; i++) {
start[i] = 0;
shape[i] = 1;
}
Dimension xdim = getXDimension();
Dimension ydim = getYDimension();
Dimension zdim = getZDimension();
Dimension tdim = getTimeDimension();
Dimension edim = getEnsembleDimension();
Dimension rtdim = getRunTimeDimension();
// construct the shape of the data volume to be read
if (rtdim != null) {
if ((rt >= 0) && (rt < rtdim.getLength())) start[rtDimOrgIndex] = rt; // fix rt
else {
shape[rtDimOrgIndex] = rtdim.getLength(); // all of rt
}
}
if (edim != null) {
if ((e >= 0) && (e < edim.getLength())) start[eDimOrgIndex] = e; // fix e
else {
shape[eDimOrgIndex] = edim.getLength(); // all of e
}
}
if (tdim != null) {
if ((t >= 0) && (t < tdim.getLength())) start[tDimOrgIndex] = t; // fix t
else {
shape[tDimOrgIndex] = tdim.getLength(); // all of t
}
}
if (zdim != null) {
if ((z >= 0) && (z < zdim.getLength())) start[zDimOrgIndex] = z; // fix z
else {
shape[zDimOrgIndex] = zdim.getLength(); // all of z
}
}
if (ydim != null) {
if ((y >= 0) && (y < ydim.getLength())) start[yDimOrgIndex] = y; // fix y
else {
shape[yDimOrgIndex] = ydim.getLength(); // all of y
}
}
if (xdim != null) {
if ((x >= 0) && (x < xdim.getLength())) // all of x
start[xDimOrgIndex] = x; // fix x
else {
shape[xDimOrgIndex] = xdim.getLength(); // all of x
}
}
if (debugArrayShape) {
System.out.println("read shape from org variable = ");
for (int i = 0; i < rank; i++)
System.out.println(
" start = "
+ start[i]
+ " shape = "
+ shape[i]
+ " name = "
+ vs.getDimension(i).getName());
}
// read it
Array dataVolume;
try {
dataVolume = vs.read(start, shape);
} catch (Exception ex) {
log.error(
"GeoGrid.getdataSlice() on dataset " + getFullName() + " " + dataset.getLocation(), ex);
throw new java.io.IOException(ex.getMessage());
}
// LOOK: the real problem is the lack of named dimensions in the Array object
// figure out correct permutation for canonical ordering for permute
List<Dimension> oldDims = new ArrayList<Dimension>(vs.getDimensions());
int[] permuteIndex = new int[dataVolume.getRank()];
int count = 0;
if (oldDims.contains(rtdim)) permuteIndex[count++] = oldDims.indexOf(rtdim);
if (oldDims.contains(edim)) permuteIndex[count++] = oldDims.indexOf(edim);
if (oldDims.contains(tdim)) permuteIndex[count++] = oldDims.indexOf(tdim);
if (oldDims.contains(zdim)) permuteIndex[count++] = oldDims.indexOf(zdim);
if (oldDims.contains(ydim)) permuteIndex[count++] = oldDims.indexOf(ydim);
if (oldDims.contains(xdim)) permuteIndex[count] = oldDims.indexOf(xdim);
if (debugArrayShape) {
System.out.println("oldDims = ");
for (Dimension oldDim : oldDims) System.out.println(" oldDim = " + oldDim.getName());
System.out.println("permute dims = ");
for (int aPermuteIndex : permuteIndex)
System.out.println(" oldDim index = " + aPermuteIndex);
}
// check to see if we need to permute
boolean needPermute = false;
for (int i = 0; i < permuteIndex.length; i++) {
if (i != permuteIndex[i]) needPermute = true;
}
// permute to the order rt,e,t,z,y,x
if (needPermute) dataVolume = dataVolume.permute(permuteIndex);
// eliminate fixed dimensions, but not all dimensions of length 1.
count = 0;
if (rtdim != null) {
if (rt >= 0) dataVolume = dataVolume.reduce(count);
else count++;
}
if (edim != null) {
if (e >= 0) dataVolume = dataVolume.reduce(count);
else count++;
}
if (tdim != null) {
if (t >= 0) dataVolume = dataVolume.reduce(count);
else count++;
}
if (zdim != null) {
if (z >= 0) dataVolume = dataVolume.reduce(count);
else count++;
}
if (ydim != null) {
if (y >= 0) dataVolume = dataVolume.reduce(count);
else count++;
}
if (xdim != null) {
if (x >= 0) dataVolume = dataVolume.reduce(count);
}
return dataVolume;
}
/**
* Build the configuration from the dataset
*
* @param ncd NetcdfDataset
* @return the trajectory configuration
*/
private static Config buildConfig(NetcdfDataset ncd) {
// already did this in isValid, but we'll keep here for later refactor
Attribute attrib = ncd.findGlobalAttributeIgnoreCase("center");
if (attrib == null) {
return null;
}
if (!attrib.isString()) {
return null;
}
if (!attrib.getStringValue().equals("UCAR/CDAAC")) {
return null;
}
// Check for start_time, stop_time
attrib = ncd.findGlobalAttributeIgnoreCase("start_time");
if (attrib == null) {
return null;
}
if (attrib.isString()) {
return null;
}
double startTime = attrib.getNumericValue().doubleValue();
attrib = ncd.findGlobalAttributeIgnoreCase("stop_time");
if (attrib == null) {
return null;
}
if (attrib.isString()) {
return null;
}
double endTime = attrib.getNumericValue().doubleValue();
// Check that only one dimension and that it is the alt dimension.
List list = ncd.getRootGroup().getDimensions();
if (list.size() != 1) {
return null;
}
Dimension d = (Dimension) list.get(0);
if (!d.getName().equals(timeDimName)) {
return null;
}
Config trajConfig = new Config();
trajConfig.setTimeDim(d);
// Check for latitude variable with time dimension and units convertable to "degrees_north".
Variable var = ncd.getRootGroup().findVariable(latVarName);
if (var == null) {
return null;
}
list = var.getDimensions();
if (list.size() != 1) {
return null;
}
d = (Dimension) list.get(0);
if (!d.getName().equals(timeDimName)) {
return null;
}
String units = var.findAttribute("units").getStringValue();
if (!SimpleUnit.isCompatible(units, "degrees_north")) {
return null;
}
trajConfig.setLatVar(var);
// Make the time Variable
int numTimes = d.getLength();
double[] times = new double[numTimes];
// Variable timeVar = new Variable(var);
// timeVar.setName(timeVarName);
VariableDS timeVar =
new VariableDS(
ncd,
ncd.getRootGroup(),
null,
timeVarName,
DataType.DOUBLE,
timeDimName,
"seconds since 1980-01-06 00:00:00",
"Time coordinate");
// Variable timeVar = new Variable(ncd, ncd.getRootGroup(), null,
// timeVarName);
// timeVar.setDataType(DataType.DOUBLE);
// timeVar.setDimensions(list);
// Attribute newUnits =
// new Attribute("units", "seconds since 1980-01-06 00:00:00");
// timeVar.addAttribute(newUnits);
timeVar.setCachedData(
Array.makeArray(DataType.DOUBLE, numTimes, endTime, ((startTime - endTime) / numTimes)),
true);
ncd.addVariable(ncd.getRootGroup(), timeVar);
trajConfig.setTimeVar(timeVar);
// Check for longitude variable with time dimension and units convertable to "degrees_east".
var = ncd.getRootGroup().findVariable(lonVarName);
if (var == null) {
return null;
}
list = var.getDimensions();
if (list.size() != 1) {
return null;
}
d = (Dimension) list.get(0);
if (!d.getName().equals(timeDimName)) {
return null;
}
units = var.findAttribute("units").getStringValue();
if (!SimpleUnit.isCompatible(units, "degrees_east")) {
return null;
}
trajConfig.setLonVar(var);
// Check for altitude variable with time dimension and units convertable to "m".
var = ncd.getRootGroup().findVariable(elevVarName);
if (var == null) {
return null;
}
list = var.getDimensions();
if (list.size() != 1) {
return null;
}
d = (Dimension) list.get(0);
if (!d.getName().equals(timeDimName)) {
return null;
}
units = var.findAttribute("units").getStringValue();
if (!SimpleUnit.isCompatible(units, "meters")) {
return null;
}
trajConfig.setElevVar(var);
trajConfig.setTrajectoryId(trajId);
return trajConfig;
}
Write2ncRect(NetcdfFile bufr, String fileOutName, boolean fill)
throws IOException, InvalidRangeException {
NetcdfFileWriteable ncfile = NetcdfFileWriteable.createNew(fileOutName, fill);
if (debug) {
System.out.println("FileWriter write " + bufr.getLocation() + " to " + fileOutName);
}
// global attributes
List<Attribute> glist = bufr.getGlobalAttributes();
for (Attribute att : glist) {
String useName = N3iosp.makeValidNetcdfObjectName(att.getName());
Attribute useAtt;
if (att.isArray()) useAtt = ncfile.addGlobalAttribute(useName, att.getValues());
else if (att.isString()) useAtt = ncfile.addGlobalAttribute(useName, att.getStringValue());
else useAtt = ncfile.addGlobalAttribute(useName, att.getNumericValue());
if (debug) System.out.println("add gatt= " + useAtt);
}
// global dimensions
Dimension recordDim = null;
Map<String, Dimension> dimHash = new HashMap<String, Dimension>();
for (Dimension oldD : bufr.getDimensions()) {
String useName = N3iosp.makeValidNetcdfObjectName(oldD.getName());
boolean isRecord = useName.equals("record");
Dimension newD = ncfile.addDimension(useName, oldD.getLength(), true, false, false);
dimHash.put(newD.getName(), newD);
if (isRecord) recordDim = newD;
if (debug) System.out.println("add dim= " + newD);
}
// Variables
Structure recordStruct = (Structure) bufr.findVariable(BufrIosp.obsRecord);
for (Variable oldVar : recordStruct.getVariables()) {
if (oldVar.getDataType() == DataType.STRUCTURE) continue;
String varName = N3iosp.makeValidNetcdfObjectName(oldVar.getShortName());
DataType newType = oldVar.getDataType();
List<Dimension> newDims = new ArrayList<Dimension>();
newDims.add(recordDim);
for (Dimension dim : oldVar.getDimensions()) {
newDims.add(ncfile.addDimension(oldVar.getShortName() + "_strlen", dim.getLength()));
}
Variable newVar = ncfile.addVariable(varName, newType, newDims);
if (debug) System.out.println("add var= " + newVar);
// attributes
List<Attribute> attList = oldVar.getAttributes();
for (Attribute att : attList) {
String useName = N3iosp.makeValidNetcdfObjectName(att.getName());
if (att.isArray()) ncfile.addVariableAttribute(varName, useName, att.getValues());
else if (att.isString())
ncfile.addVariableAttribute(varName, useName, att.getStringValue());
else ncfile.addVariableAttribute(varName, useName, att.getNumericValue());
}
}
// int max_seq = countSeq(recordStruct);
// Dimension seqD = ncfile.addDimension("level", max_seq);
for (Variable v : recordStruct.getVariables()) {
if (v.getDataType() != DataType.STRUCTURE) continue;
String structName = N3iosp.makeValidNetcdfObjectName(v.getShortName());
int shape[] = v.getShape();
Dimension structDim = ncfile.addDimension(structName, shape[0]);
Structure struct = (Structure) v;
for (Variable seqVar : struct.getVariables()) {
String varName = N3iosp.makeValidNetcdfObjectName(seqVar.getShortName() + "-" + structName);
DataType newType = seqVar.getDataType();
List<Dimension> newDims = new ArrayList<Dimension>();
newDims.add(recordDim);
newDims.add(structDim);
for (Dimension dim : seqVar.getDimensions()) {
newDims.add(ncfile.addDimension(seqVar.getShortName() + "_strlen", dim.getLength()));
}
Variable newVar = ncfile.addVariable(varName, newType, newDims);
if (debug) System.out.println("add var= " + newVar);
// attributes
List<Attribute> attList = seqVar.getAttributes();
for (Attribute att : attList) {
String useName = N3iosp.makeValidNetcdfObjectName(att.getName());
if (att.isArray()) ncfile.addVariableAttribute(varName, useName, att.getValues());
else if (att.isString())
ncfile.addVariableAttribute(varName, useName, att.getStringValue());
else ncfile.addVariableAttribute(varName, useName, att.getNumericValue());
}
}
}
// create the file
ncfile.create();
if (debug) System.out.println("File Out= " + ncfile.toString());
// boolean ok = (Boolean) ncfile.sendIospMessage(NetcdfFile.IOSP_MESSAGE_ADD_RECORD_STRUCTURE);
double total = copyVarData(ncfile, recordStruct);
ncfile.flush();
System.out.println("FileWriter done total bytes = " + total);
ncfile.close();
}
